I wonder if OP didn't realise there was this _Show Hidden Files_ option and their .git was indeed backed up.

That would be nice, they'd be able to get their history back!

> .git files seem to still be backing up on my machine

Try checking bzexcluderules_editable.xml. A few years ago, Backblaze would back up .git folders for Mac but not Windows. Not sure if this is still the case.